Skeletal muscle glycogen synthase (encoded by GYS1 on chromosome 19q13.3) is the rate limiting enzyme in insulin-mediated non-oxidative glucose disposal. Our previous studies demonstrated an impairment of insulin- stimulated GYS1 activities in insulin resistant Pimas, and associations of NIDDM with the GYS1 locus were reported recently in Finish and Japanese populations. We have performed linkage and association analyses of GYS1 and seven additional DNA markers on 19q with NIDDM and with parameters of insulin action in the Pimas. We have found a significant association of NIDDM with GYS1 in the Pima Indians. We have performed a detailed comparative analysis of the GYS1 gene, mRNA, and protein product in insulin sensitive and insulin resistant Pimas. No mutations in GYS1 coding sequences were detected, neither did we find alterations of GYS1 mRNA expression, or of its basal enzymatic activity in insulin resistant Pimas. These results contrasted with a 25% reduction of immunoreactive GYS1 protein in insulin resistant subjects as detected by western blotting. Because no mutations were detected in DNA encoding this epitope, the difference in immunoreactivity may reflect post- translational modification(s) of the protein rather than a difference in the gene itself. We conclude that our data do not indicate alterations in the GYS1 gene as the cause for the observed association. It is possible that a different locus near GYS1 may be the contributing genetic element.